Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 209326 DVU0390 glycolate oxidase, subunit GlcD, putative
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >MicrobesOnline__882:209326 Length = 460 Score = 79.0 bits (193), Expect = 3e-19 Identities = 111/411 (27%), Positives = 164/411 (39%), Gaps = 69/411 (16%) Query: 19 IRHATGTRTPLRLRGGGSKDFYG--QHPQGTLLDTRAYSGIVDYDPPELV--ITARCGTP 74 +R AT R P+ RGGG+ G G +L + + D LV + A C T Sbjct: 60 MRLATEHRFPVIPRGGGTGLAGGCLALMGGVVLSVERMNRVRAIDTRNLVAEVDAGCITQ 119 Query: 75 LAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGT 134 + AA A F PP + G D +T+GG VA GP G RD+VLG Sbjct: 120 TLRDAAAAAN-----LFYPPDPA----GMDRSTVGGNVATNAGGPACVKYGVTRDYVLGV 170 Query: 135 RVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFAL 194 + G++L G + K V GYD++ L+ GS GTLG+I +++K++P+P + A Sbjct: 171 EAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVITGLTMKLIPLPAATVGMAVAF 230 Query: 195 DEAAALDR--LNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARL------GGEAV 246 + + R G LP A L L + AR L G A Sbjct: 231 ADMPSAMRAVAAVLGAGHLPSAIEFMDHRCLALVGEMLPFPVPGARPSLLIIELDGQRAT 290 Query: 247 DAAQADALWRALREH--SHAFFAPVQAGRA-LW--------------------RIAVPTT 283 Q DA+ RE + AP A RA +W +AVP Sbjct: 291 IEPQLDAVAAICREQGATQVLPAPTDAERATIWGVRRQVSLRIHDYAGLYLSEDVAVPLV 350 Query: 284 AAP---LALP------GGQLIEWG--GGQRWWLGGSDSAADS------AIVRAAAKAAGG 326 A LP G ++ +G G L + S+ D+ +V A + Sbjct: 351 AIADLVAELPAFEERYGLEIFAFGHAGDGNIHLNVTSSSTDNRERAEEGVVALARRVVEL 410 Query: 327 HATLFRNGDKAVG------VFTPLSAPVAAIHQRLKATFDPAGIFNPQRMY 371 T+ +G+ +G V LSA A+ + ++ FDP GI NP +++ Sbjct: 411 GGTI--SGEHGIGEAKKHLVPLELSARSIALQKGIRGVFDPLGIMNPGKVF 459 Lambda K H 0.321 0.136 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 387 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 374 Length of database: 460 Length adjustment: 31 Effective length of query: 343 Effective length of database: 429 Effective search space: 147147 Effective search space used: 147147 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory